https://github.com/veupathdb/vdi-plugin-rnaseq
https://github.com/veupathdb/vdi-plugin-rnaseq
Last synced: 9 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/veupathdb/vdi-plugin-rnaseq
- Owner: VEuPathDB
- License: apache-2.0
- Created: 2023-03-24T16:06:09.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-06-26T16:59:38.000Z (12 months ago)
- Last Synced: 2025-08-06T01:31:36.242Z (11 months ago)
- Language: Perl
- Size: 159 KB
- Stars: 0
- Watchers: 17
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: readme.adoc
- License: license
Awesome Lists containing this project
README
= VDI RNA Seq Handler
:icons: font
ifdef::env-github[]
:tip-caption: :bulb:
:note-caption: :information_source:
:important-caption: :heavy_exclamation_mark:
:caution-caption: :fire:
:warning-caption: :warning:
endif::[]
This is the VDI Handler for RNA Seq datasets. These datasets contain FPKM data in .txt files, and optionally bigwig files used for genome browser tracks.
See the https://github.com/VEuPathDB/vdi-handler-plugin-example[VDI Handler Example repo] for background.
For more details about the scripts themselves and their inputs and outputs see
the https://github.com/VEuPathDB/vdi-plugin-handler-server[VDI Plugin Handler Server]
readme.
The `import` script does its best to validate the dataset. On the assumption that the dataset is provided by the VEuPathDB RNA Seq Exporter, we hope that it was constructed validly. It is possible the validator will miss ways the dataset could go wrong.
Here is a manifest file from a stranded dataset
```
SRR5260550.fastq-forward SRR5260550.fastq-forward.bw firststrand
SRR5260550.fastq-reverse SRR5260550.fastq-reverse.bw secondstrand
SRR5260551.fastq-forward SRR5260551.fastq-forward.bw firststrand
SRR5260551.fastq-reverse SRR5260551.fastq-reverse.bw secondstrand
SRR5260552.fastq-forward SRR5260552.fastq-forward.bw firststrand
SRR5260552.fastq-reverse SRR5260552.fastq-reverse.bw secondstrand
SRR5260550.fastq-one SRR5260550.fastq-one.txt sense
SRR5260550.fastq-two SRR5260550.fastq-two.txt antisense
SRR5260551.fastq-one SRR5260551.fastq-one.txt sense
SRR5260551.fastq-two SRR5260551.fastq-two.txt antisense
SRR5260552.fastq-one SRR5260552.fastq-one.txt sense
SRR5260552.fastq-two SRR5260552.fastq-two.txt antisense
```